At the outbreak of the war, Malloy's trainees became part of the "Madison Guards" militia company which joined the 1st Wisconsin Infantry Regiment.

[4]: 443–444 That December, Malloy was promoted to lieutenant colonel for the newly organized 17th Wisconsin Infantry Regiment—the "Irish Brigade".

With the 17th Wisconsin, Malloy moved to the western theater of the war and participated in the sieges of Corinth and Vicksburg in Mississippi.

At Chattanooga, a provisional division was organized of these returning veterans and new recruits, and Malloy was placed in command of a brigade composed of the men who were ultimately bound for regiments in XVII Corps.

Malloy's brigade was ordered to guard duty in the Tunnel Hill and Ringgold region, but upon learning of Confederate general John Bell Hood's disposition to attack Nashville, Tennessee, they rode by rail back north to assist in the defense of that city in the Battle of Nashville.

[5]: 654 After some additional work in Alabama, the provisional division was sent back to Baltimore, by way of Ohio, and took steamboats to Beaufort, North Carolina, arriving February 8, 1865.

[2][5]: 654–655  For his part in the Battle of Wyse Fork, Malloy received mention and compliments in the account of the division commander, General Samuel P.

[7][note 1] Colonel Malloy's own account of the battle can be found in the Official War Records, Series 1, Volume 47, Part 1, item 266.

[7] After the reunion with Sherman's army, Malloy resumed command of the 17th Wisconsin Infantry for the remaining days of the war.

[2] Malloy resigned from the Army in August 1870, and accepted an appointment from the state government of Texas to aid in Reconstruction.